Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.

Changes in functional gene structure and metabolic potential of the microbial community in biological soil crusts along a revegetation chronosequence in the Tengger Desert

Biocrusts affect preferential flow and water holding capacity by regulating soil properties in Ultisols from subtropical China

Biological soil crusts composed of cyanobacteria, green algae, bryophytes, and lichens colonize soils in arid and semiarid ecosystems worldwide and are responsible for significant N input to the soils of these ecosystems. Soil crusts also colonize active sand dunes in more humid regions, but studies of structure and function of such sand dune crusts are lacking. We identified the cyanobacterial, algal, and bryophytic constituents and N production and leachates of biological soil crusts that colonize beach dunes at the Indiana Dunes National Lakeshore along southern Lake Michigan in Indiana, USA. To determine the role of these crusts in this system, we conducted a greenhouse experiment in which intact soil cores with biological crusts were subjected to artificial rainfall over a full growing season. The volume and N content of leachate from the cores were quantified in relation to degree of crust development, taxonomic composition, rainfall volume and intensity, light intensity, and the presence of plant litter. Net N throughput significantly exceeded N inputs to cores in rainwater. Net N outputs from crusts to subsurface soil ranged from 0. 01 to 0.19 g NH 4 + -N m−2 yr−1 and 0.01 to 0.61 g NO 3 – N m−2 yr−1. Thus, total inorganic N inputs associated with biological soil crusts ranged from 0.02 g N m−2 yr−1 to 0.8 g N m−2 yr−1. High volume (≥2 cm) rainfall resulted in more N leaching than low volume events, and plant litter added over the surface of crusted soil cores significantly increased the amount of N in leachate. Exploratory path analysis revealed direct and indirect linkages among environmental factors, crust development, and crust composition in regulating the throughput of H2O and N from these intact soil cores. Biological soil crusts at this site, combined with other properties of the soil surface, substantially increase N inputs to this water- and nutrient-limited sand dune ecosystem.

Microbial survival strategies in biological soil crusts of polymetallic tailing wetlands

Manganese enhances the immobilization of trace cadmium from irrigation water in biological soil crust

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

Simple SummaryMicrobial communities play a significant role in the functioning of the ecosystem in the cold mountain desert of Eastern Pamir, a region that is characterized by extreme environments with limited nutrient and water availability and sparse vegetation. This study aims to investigate the taxonomic composition and structure of bacterial endolithic (rock matrix colonizing) assemblages and soil-inhabiting communities that occur in the Eastern Pamir Mountains, and to compare the composition and structure of both types of communities looking for general patterns and trying to identify the connectivity between these types of microbial assemblages. The taxonomic composition of Pamirian endolithic communities and soil-inhabiting microbial consortia (biocrust communities) exhibit similarities to communities from cold and hot deserts, but they also harbor taxa, which are possibly novel species or which, so far, lack reference sequences in the databases. The endolithic communities occurring in three subregions of Eastern Pamir are characterized by high heterogeneity and cannot be grouped according to the subregion, while the distribution of Cyanobacteria in the soil crusts demonstrates the similarities between the communities within the subregion reflecting regional differences. We also found connectivity between both habitats concerning the occurrence the same taxa (e.g., Cyanobacteria).Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria–Proteobacteria–Bacteroidetes–Chloroflexi–Cyanobacteria, while the BSCs’ can be described as Proteobacteria–Actinobacteria–Bacteroidetes–Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of Chroococcidiopsis, Gloeocapsopsis and Wilmottia. Despite the niches’ specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.

Immobilization of metal(loid)s from acid mine drainage by biological soil crusts through biomineralization.

Biological soil crusts (BSCs) cover >35% of the Earth’s land area and contribute to important ecological functions in arid and semiarid ecosystems, including erosion reduction, hydrological cycling, and nutrient cycling. Artificial rapid cultivation of BSCs can provide a novel alternative to traditional biological methods for controlling soil and water loss such as the planting of trees, shrubs, and grasses. At present, little is known regarding the cultivation of BSCs in the field due to lack of knowledge regarding the influencing factors that control BSCs growth. Thus, we determined the effects of various environmental factors (shade; watering; N, P, K, and Ca concentrations) on the growth of cyanobacteria-dominated BSCs from the Sonoran Desert in the southwestern United States. The soil surface changes and chlorophyll a concentrations were used as proxies of BSC growth and development. After 4 months, five factors were found to impact BSC growth with the following order of importance: NH4NO3 ≈ watering frequency>shading>CaCO3 ≈ KH2PO4. The soil water content was the primary positive factor affecting BSC growth, and BSCs that were watered every 5 days harbored greater biomass than those watered every 10 days. Groups that received NH4NO3 consistently exhibited poor growth, suggesting that fixed N amendment may suppress BSC growth. The effect of shading on the BSC biomass was inconsistent and depended on many factors including the soil water content and availability of nutrients. KH2PO4 and CaCO3 had nonsignificant effects on BSC growth. Collectively, our results indicate that the rapid restoration of BSCs can be controlled and realized by artificial “broadcasting” cultivation through the optimization of environmental factors.

Biological soil crusts (BSCs) are distributed worldwide in all semiarid and arid lands, where they play a determinant role in element cycling and soil development. Although much work has concentrated on BSC microbial communities, free-living fungi have been hitherto largely overlooked. The aim of this study was to examine the fungal biodiversity, by cultural-dependent and cultural-independent approaches, in thirteen samples of Arctic BSCs collected at different sites in the Alpine Tarfala Valley, located on the slopes of Kebnekaise, the highest mountain in northern Scandinavia. Isolated fungi were identified by both microscopic observation and molecular approaches. Data revealed that the fungal assemblage composition was homogeneous among the BSCs analyzed, with low biodiversity and the presence of a few dominant species; the majority of fungi isolated belonged to the Ascomycota, and Cryptococcus gilvescens and Pezoloma ericae were the most frequently-recorded species. Ecological considerations for the species involved and the implication of our findings for future fungal research in BSCs are put forward.

Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.

Divergent determinants on interannual variability of terrestrial water cycle across the globe

Vapor pressure deficit (VPD) is critical to the carbon–water cycle of an ecosystem, which is widely used in various hydrological cycles, vegetation carbon cycles, and evapotranspiration-estimation models. However, few studies on VPD have been conducted. Most regions of China are experiencing accelerated urbanization and continuing increased interannual variations in atmospheric parameters, such as temperature and humidity. An in-depth study on the variation and dominant factors of VPD in different seasons and climate regions will provide a scientific basis for the study of climate, ecology, and vegetation models. Such a study will also help improve environmental management in different climate regions to achieve ecologically sustainable development. Based on the monthly meteorological observation data of more than 600 stations in China, combined with the Mann–Kendall test, multiple linear regression, and other methods, this study analyzed the spatio–temporal variation pattern of VPD in the four climate regions (i.e., arid, humid, semiarid, and subhumid) of China from 1980 to 2018 to detect the dominant meteorological factors affecting the variation of VPD. The results showed that for the last 40 years, the distribution of VPD in Chinahadd spatial and seasonal differences. For all four climate regions, VPD had the characteristics of “summer > spring > autumn > winter.” The distribution of VPD in summer and winter is opposite in the humid and arid regions of China. That is, the VPD in spring and summer gradually increased from the humid region to the arid region; whereas, it gradually decreased from the humid region to the arid region in winter. VPD exhibited an upward trend in most areas of China in the four seasons, particularly in the Yellow River Basin and southeast coastal areas in spring and summer. Moreover, the VPD of the four climate regions increased abruptly in the early 21st century. Among them, the humid region had an earlier mutation year (1996), and the arid region had a later mutation year (2004); the increase in the arid region was the highest, at approximately 0.04 kPa/10 a). These phenomena indicate that the atmosphere has become drier, and to determine the cause of this phenomenon, we analyzed the contribution rate of meteorological factors to VPD. The results showed that the dominant factors affecting the increase in VPD are different in different climate regions and seasons, but overall, changes in air temperature and absolute humidity are the main factors affecting the interannual change of VPD in China. After 2000, the dominant factors affecting VPD in subhumid and semiarid and other areas are temperature and absolute humidity, respectively.

Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.

Concostrina-Zubiri, L., Martínez, I., Huber-Sannwald, E., Escudero, A. 2013. Biological Soil Crust effects and responses in arid ecosystems: recent advances at the species level. Ecosistemas 22(3):95-000. Doi.: 10.7818/ECOS.2013.22-3.13. Biological soil crusts (BSCs) constitute a complex component of the ecosystem formed by different organisms (lichens, mosses, liverworts, cyanobacteria, fungi, algae) associated with soil surface. These communities are present in a wide variety of ecosystems; however, their abundance is generally higher in arid environments with sparse vegetation cover. In these ecosystems, BSCs greatly contribute to biodiversity and ecosystem functioning. Due to technical difficulties in species identification, most studies on BSCs have been carried out at community and morphotype levels. These studies have emphasized the potential role of BSCs in defining ecosystem structure and functioning by: interacting with topsoil layers and other soil organisms, participating in carbon and nitrogen fixation, and also in hydrological and nutrient cycling. Notwithstanding, recent advances in our knowledge about BSCs show substantial and interesting differences in the ecology and functional roles of BSC species, with marked implications in the management and conservation of these communities and their ecosystems. Particularly, it has been observed that BSC presence, abundance and frequency respond differently to diverse environmental factors (climatic variables, soil type, presence of vascular plants, and grazing disturbance - natural recovery) at the species level, and also do BSC effects on topsoil properties.